The Senate has passed the bill known as the "water trigger amendment".

Passage of the Environment Protection and Biodiversity Conservation Act amendment occurred on Wednesday.

The legislation is expected to receive Royal Assent before the end of June, making it law.

The bill's passage now means the Commonwealth is responsible for ensuring water systems are not impacted by major coal seam gas and coal mining projects.

Where previously the Commonwealth had no legal authority over major coal and CSG projects, it is now prevented from devolving back to the States scientific assessment.

Now, the Commonwealth's Independent Expert Scientific Committee will assess the efficacy of major projects and the likely impact those developments might have on water resources.

The amendment was introduced by federal New England MP, Tony Windsor, in the House of Representatives in late March.

The Coalition opposed the amendment in the Lower House.

Liberal Senator, Simon Birmingham, says there are many aspects of the water trigger amendment that trouble him.

But he says he accepts there are community concerns about the impact that some major resource projects can have on groundwater systems.

"Whilst the Coalition has significant concerns about the way the Government and the Greens' have conducted this debate, in fact, grave concerns about the application of the gag and the guillotine," he said.

"We, nonetheless, acknowledge there are genuine community concerns that surround the issue of coal seam gas development and large coal mining development and what their impact may be."

During debate on the bill, Senator Birmingham, told the Senate the Coalition will work hard to protect water resources if it wins the September federal election.

He says there'll be no duplication between the Commonwealth and the States on regulations designed to protect groundwater resources.

"Despite our vehement opposition to the amendment made by Mr Windsor we support the new water trigger and we'll make sure, should we be elected to government, that it's applied in a robust way," he said.

"That will mean eliminating State and Commonwealth overlapping of environmental regulation."

Tony Windsor says he's relieved the Commonwealth must now be engaged in water resource protection when it comes to big mining and gas projects.

"I'm very pleased to have been part of a process about the impacts on water of some of these activities and wanting some scientific rigour before decisions are made," he said.

"So, I think it's a real victory for community concern and community effort."

But Tony Windsor says the future of the water trigger legislation will be determined by the make-up of the Senate after the September federal election.

"I don't think the Coalition will have control of the Senate and unless they have control of the Senate they won't be able to reverse this process," he said.

"So, the make-up of the Senate at the next election is as important as the make-up of the House of Representatives and that's up to the people."

Liverpool Plains farmer, Tim Duddy, says he anticipates Shenhua, Santos and BHP-Billiton will now have their projects referred to the Independent Expert Scientific Committee.

He says the outcome will be more robust assessments which, he says, will be good for the companies, local communities, farmers and the environment.

"Some of those water resources are several million years old and it would be ridiculous to contemplate ruining them for the sake of two or three years to find out what you're impacts are going to be," he said.

"If the mining companies have to wait a little longer before they get their projects up it's not relevant and the fact of the matter is here we have enormously significant agricultural water resources and this bill goes a long way to doing that."

Tony Windsor says he hopes the NSW government acts quickly to accommodate the new amendment to federal environment law.

"I'd suggest that Barry O'Farrell should look very, very seriously at this [because] it is interests of all people in NSW that we have a process based on science," he said.

"If they allow activities to go ahead in high-risk areas one failure will mean death to the industry and more importantly it could have devastating consequences to agriculture and water resources generally."

ABC News sought comment from the Minister for Energy and Resources, Chris Hartcher; the Minister for Planning, Brad Hazzard; the NSW Minerals Council; and the Minerals Council of Australia.